Mike Morgan
| Snapshot Date: 2024-05-08 14:00:19 -0400 (Wed, 08 May 2024) |
| git_url: https://git.bioconductor.org/packages/miloR |
| git_branch: RELEASE_3_19 |
| git_last_commit: 97eb8a7 |
| git_last_commit_date: 2024-04-30 11:34:02 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-09 11:41:06 -0400 (Thu, 09 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4748 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4484 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4514 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4480 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1271/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| miloR 2.0.0 (landing page) Mike Morgan
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the miloR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/miloR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: miloR |
| Version: 2.0.0 |
| Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL miloR |
| StartedAt: 2024-05-08 20:58:26 -0000 (Wed, 08 May 2024) |
| EndedAt: 2024-05-08 21:01:54 -0000 (Wed, 08 May 2024) |
| EllapsedTime: 207.7 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL miloR
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* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘miloR’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppArmadillo/include' -I/usr/local/include -g -O2 -Wall -std=gnu++11 -fopenmp -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppArmadillo/include' -I/usr/local/include -g -O2 -Wall -std=gnu++11 -fopenmp -fPIC -g -O2 -Wall -c computeMatrices.cpp -o computeMatrices.o
computeMatrices.cpp: In function ‘arma::mat initialiseG(Rcpp::List, arma::vec)’:
computeMatrices.cpp:135:30: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
135 | for(unsigned long k=0; k < stot; k++){
| ~~^~~~~~
computeMatrices.cpp:143:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
143 | for(int l=0; l < q; l++){
| ~~^~~
computeMatrices.cpp: In function ‘arma::mat invGmat(Rcpp::List, arma::vec)’:
computeMatrices.cpp:327:30: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
327 | for(unsigned long k=0; k < stot; k++){
| ~~^~~~~~
computeMatrices.cpp:335:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
335 | for(int l=0; l < q; l++){
| ~~^~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppArmadillo/include' -I/usr/local/include -g -O2 -Wall -std=gnu++11 -fopenmp -fPIC -g -O2 -Wall -c fitGeneticPLGlmm.cpp -o fitGeneticPLGlmm.o
fitGeneticPLGlmm.cpp: In function ‘Rcpp::List fitGeneticPLGlmm(const mat&, const mat&, const mat&, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::mat, const vec&, Rcpp::List, double, const List&, double, const bool&, const int&, std::string, std::string)’:
fitGeneticPLGlmm.cpp:197:10: warning: unused variable ‘_phi_est’ [-Wunused-variable]
197 | bool _phi_est = true; // control if we re-estimate phi or not
| ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppArmadillo/include' -I/usr/local/include -g -O2 -Wall -std=gnu++11 -fopenmp -fPIC -g -O2 -Wall -c fitPLGlmm.cpp -o fitPLGlmm.o
fitPLGlmm.cpp: In function ‘Rcpp::List fitPLGlmm(const mat&, const mat&, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::mat, const vec&, Rcpp::List, double, const List&, double, const bool&, const int&, std::string, std::string)’:
fitPLGlmm.cpp:177:10: warning: unused variable ‘_phi_est’ [-Wunused-variable]
177 | bool _phi_est = true; // control if we re-estimate phi or not
| ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppArmadillo/include' -I/usr/local/include -g -O2 -Wall -std=gnu++11 -fopenmp -fPIC -g -O2 -Wall -c inference.cpp -o inference.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppArmadillo/include' -I/usr/local/include -g -O2 -Wall -std=gnu++11 -fopenmp -fPIC -g -O2 -Wall -c invertPseudoVar.cpp -o invertPseudoVar.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppArmadillo/include' -I/usr/local/include -g -O2 -Wall -std=gnu++11 -fopenmp -fPIC -g -O2 -Wall -c multiP.cpp -o multiP.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppArmadillo/include' -I/usr/local/include -g -O2 -Wall -std=gnu++11 -fopenmp -fPIC -g -O2 -Wall -c paramEst.cpp -o paramEst.o
paramEst.cpp: In function ‘arma::vec sigmaScoreREML_arma(const List&, const vec&, const mat&, const vec&, const mat&, const mat&)’:
paramEst.cpp:29:33: warning: left operand of comma operator has no effect [-Wunused-value]
29 | double rhs = 0.5 * mid1[0, 0];
| ^
paramEst.cpp: In function ‘arma::vec estHasemanElstonGenetic(const mat&, const mat&, const List&, const vec&, const mat&)’:
paramEst.cpp:258:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
258 | for (int i = 0; i < n; i++) {
| ~~^~~
paramEst.cpp:259:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
259 | for (int j = i; j < n; j++) {
| ~~^~~
paramEst.cpp:252:18: warning: unused variable ‘i’ [-Wunused-variable]
252 | unsigned int i, j; // Declare loop variables i and j for OpenMP
| ^
paramEst.cpp:252:21: warning: unused variable ‘j’ [-Wunused-variable]
252 | unsigned int i, j; // Declare loop variables i and j for OpenMP
| ^
paramEst.cpp:253:12: warning: unused variable ‘_ycovij’ [-Wunused-variable]
253 | double _ycovij; // Declare temp_value
| ^~~~~~~
paramEst.cpp: In function ‘arma::vec estHasemanElston(const mat&, const mat&, const List&, const vec&)’:
paramEst.cpp:302:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
302 | for (int i = 0; i < n; i++) {
| ~~^~~
paramEst.cpp:303:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
303 | for (int j = i; j < n; j++) {
| ~~^~~
paramEst.cpp:294:18: warning: unused variable ‘i’ [-Wunused-variable]
294 | unsigned int i, j; // Declare loop variables i and j for OpenMP
| ^
paramEst.cpp:294:21: warning: unused variable ‘j’ [-Wunused-variable]
294 | unsigned int i, j; // Declare loop variables i and j for OpenMP
| ^
paramEst.cpp:295:12: warning: unused variable ‘_ycovij’ [-Wunused-variable]
295 | double _ycovij; // Declare temp_value
| ^~~~~~~
paramEst.cpp: In function ‘arma::vec estHasemanElstonConstrained(const mat&, const mat&, const List&, const vec&, arma::vec, const int&)’:
paramEst.cpp:381:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
381 | for (int i = 0; i < n; i++) {
| ~~^~~
paramEst.cpp:382:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
382 | for (int j = i; j < n; j++) {
| ~~^~~
paramEst.cpp:373:18: warning: unused variable ‘i’ [-Wunused-variable]
373 | unsigned int i, j; // Declare loop variables i and j for OpenMP
| ^
paramEst.cpp:373:21: warning: unused variable ‘j’ [-Wunused-variable]
373 | unsigned int i, j; // Declare loop variables i and j for OpenMP
| ^
paramEst.cpp:374:12: warning: unused variable ‘_ycovij’ [-Wunused-variable]
374 | double _ycovij; // Declare temp_value
| ^~~~~~~
paramEst.cpp: In function ‘arma::vec estHasemanElstonConstrainedGenetic(const mat&, const mat&, const List&, const vec&, const mat&, arma::vec, const int&)’:
paramEst.cpp:490:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
490 | for (int i = 0; i < n; i++) {
| ~~^~~
paramEst.cpp:491:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
491 | for (int j = i; j < n; j++) {
| ~~^~~
paramEst.cpp:484:18: warning: unused variable ‘i’ [-Wunused-variable]
484 | unsigned int i, j; // Declare loop variables i and j for OpenMP
| ^
paramEst.cpp:484:21: warning: unused variable ‘j’ [-Wunused-variable]
484 | unsigned int i, j; // Declare loop variables i and j for OpenMP
| ^
paramEst.cpp:485:12: warning: unused variable ‘_ycovij’ [-Wunused-variable]
485 | double _ycovij; // Declare temp_value
| ^~~~~~~
paramEst.cpp: In function ‘arma::vec nnlsSolve(const mat&, const vec&, arma::vec, const int&)’:
paramEst.cpp:549:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
549 | for(int i=0; i < m; i++){
| ~~^~~
paramEst.cpp:559:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
559 | for(int i=0; i < m; i++){
| ~~^~~
paramEst.cpp:587:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
587 | for(int i=0; i < m; i++){
| ~~^~~
paramEst.cpp:623:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
623 | for(int i=0; i < m; i++){
| ~~^~~
paramEst.cpp:543:18: warning: variable ‘inner_count’ set but not used [-Wunused-but-set-variable]
543 | unsigned int inner_count = 0;
| ^~~~~~~~~~~
paramEst.cpp:544:18: warning: unused variable ‘outer_count’ [-Wunused-variable]
544 | unsigned int outer_count = 0;
| ^~~~~~~~~~~
paramEst.cpp: In function ‘arma::mat vectoriseZ(const mat&, const List&, const mat&)’:
paramEst.cpp:688:9: warning: unused variable ‘j’ [-Wunused-variable]
688 | int j, k, l, a;
| ^
paramEst.cpp:688:12: warning: unused variable ‘k’ [-Wunused-variable]
688 | int j, k, l, a;
| ^
paramEst.cpp:688:15: warning: unused variable ‘l’ [-Wunused-variable]
688 | int j, k, l, a;
| ^
paramEst.cpp:688:18: warning: unused variable ‘a’ [-Wunused-variable]
688 | int j, k, l, a;
| ^
paramEst.cpp: In function ‘double phiLineSearch(double, double, double, const int&, const vec&, const mat&, double, const vec&, const vec&, const vec&)’:
paramEst.cpp:866:12: warning: unused variable ‘half_logli’ [-Wunused-variable]
866 | double half_logli = nbLogLik(mu, disp/2.0, y) - normlihood;
| ^~~~~~~~~~
paramEst.cpp:871:10: warning: unused variable ‘comp_vals’ [-Wunused-variable]
871 | bool comp_vals = false;
| ^~~~~~~~~
paramEst.cpp: In function ‘arma::mat vectoriseZ(const mat&, const List&, const mat&)’:
paramEst.cpp:714:21: warning: ‘temp_value’ may be used uninitialized in this function [-Wmaybe-uninitialized]
714 | #pragma omp parallel for reduction(+:temp_value)
| ^~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppArmadillo/include' -I/usr/local/include -g -O2 -Wall -std=gnu++11 -fopenmp -fPIC -g -O2 -Wall -c pseudovarPartial.cpp -o pseudovarPartial.o
pseudovarPartial.cpp: In function ‘Rcpp::List pseudovarPartial_P(Rcpp::List, const mat&)’:
pseudovarPartial.cpp:58:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
58 | for (int j = 0; j < n; j++) {
| ~~^~~
pseudovarPartial.cpp:61:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
61 | for (int k = 0; k < n; k++) {
| ~~^~~
pseudovarPartial.cpp:64:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
64 | for(int a=0; a < n; a++){
| ~~^~~
pseudovarPartial.cpp:60:21: warning: ‘temp_value’ may be used uninitialized in this function [-Wmaybe-uninitialized]
60 | #pragma omp parallel for reduction(+:temp_value)
| ^~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppArmadillo/include' -I/usr/local/include -g -O2 -Wall -std=gnu++11 -fopenmp -fPIC -g -O2 -Wall -c utils.cpp -o utils.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -L/usr/local/lib -o miloR.so RcppExports.o computeMatrices.o fitGeneticPLGlmm.o fitPLGlmm.o inference.o invertPseudoVar.o multiP.o paramEst.o pseudovarPartial.o utils.o -lopenblas -lgfortran -lm -fopenmp -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-miloR/00new/miloR/libs
** R
** data
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘graph’ in package ‘miloR’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (miloR)